Biological network exploration with Cytoscape 3.
Biological network exploration with Cytoscape 3.
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DOI：
10.1002/0471250953.bi0813s47
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发表时间：
2014-09-08
影响因子：
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通讯作者：
Bader, Gary D
中科院分区：
文献类型：
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作者：
Su, Gang;Morris, John H;Demchak, Barry;Bader, Gary D
Cytoscape 是最流行的开源软件工具之一，用于对由蛋白质、基因和其他类型的相互作用组成的生物医学网络进行可视化探索。它为研究人员提供了一个多功能的交互式可视化界面，用于探索由不同注释和实验数据支持的复杂生物互连，从而促进预测基因功能和通路构建等研究任务。 Cytoscape 提供加载、可视化、搜索、过滤和保存网络的核心功能，数百个应用程序扩展了此功能以满足特定的研究需求。最新一代的Cytoscape（3.0及更高版本）相对于之前的版本在功能、用户界面和性能方面都有了实质性的改进。该协议旨在通过基本 Cytoscape 功能的特定协议来启动新用户，例如安装 Cytoscape 和 Cytoscape 应用程序、加载数据、可视化和导航网络、可视化网络相关数据（属性）和识别集群。它还强调了有利于经验丰富的用户的新功能。
Cytoscape is one of the most popular open-source software tools for the visual exploration of biomedical networks composed of protein, gene and other types of interactions. It offers researchers a versatile and interactive visualization interface for exploring complex biological interconnections supported by diverse annotation and experimental data, thereby facilitating research tasks such as predicting gene function and pathway construction. Cytoscape provides core functionality to load, visualize, search, filter and save networks, and hundreds of Apps extend this functionality to address specific research needs. The latest generation of Cytoscape (version 3.0 and later) has substantial improvements in function, user interface and performance relative to previous versions. This protocol aims to jump-start new users with specific protocols for basic Cytoscape functions, such as installing Cytoscape and Cytoscape Apps, loading data, visualizing and navigating the network, visualizing network associated data (attributes) and identifying clusters. It also highlights new features that benefit experienced users.